Opinion: our desire for cleanliness means we're not exposed to as many microbes as before and this is affecting our ability to fight serious infections

Would you go to war with an army that has never seen action? That could be what’s happening in our current, hyper-clean life: we are not exposed to as many microbes as our ancestors would have been. Although this may appear to contribute positively to our health, it is more than likely affecting it in ways that are only becoming clear now.

Our immune system is a personalised army that protects us against the threats of viruses, bacteria, fungi and parasites. Like a real army, our immune system needs to be trained, otherwise it won’t be able to do its job effectively.

Unfortunately, our immune system can also get it wrong and start attacking harmless compounds instead of dangerous microbes, thus giving rise to allergies. Worse, it can even attack our own organs and cause us to develop autoimmune diseases such as multiple sclerosis or Type I diabetes. The incidence of allergies and autoimmune diseases has risen steadily in western countries since the 1960s and several theories have been put forward to try to explain this.

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The idea of training being necessary for any type of army convinced scientists back in the late 1980s that we may simply have become too clean for our own good. The hygiene hypothesis, as the theory was known, stated that your immune system would not get properly educated and would start attacking at random when you lived in an environment where very few microbes were present.

The hygiene hypothesis was seductive. Clearly, our immune system learns from having to deal with the different types of threats it is exposed to. If it never sees any threats, then it will never learn how to fight them appropriately.

However, there were facts that the hygiene hypothesis could not explain. Developing colds, diarrhoea, otitis, pneumonia or other serious infections at an early age did not prevent children from suffering from allergies later in life. Their immune systems were clearly active and fighting the infections, but that didn’t prevent them from malfunctioning later.

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It became clear then than fighting serious infections was more like open war than a military exercise. So what would be the immune system equivalent of a drill?

We often forget that we carry with us more bacterial than human cells. Microbes are a constant presence in our body, and a good one too. They are not our enemies but our allies. They help us digest our food and keep dangerous germs at bay. We are indeed ecosystems and our microbiota – the group of microbes living in our body – is part of our bodies and as essential to their health as the liver or the kidneys are.

The different kinds of bacteria and other microbes that live inside us have been steadily declining since the 1960s

Recent research has shown that it is the microbiota that educates our immune systems, providing the drills and military exercises. Because the microbiota is needed for the healthy functioning of our bodies, it needs to convince our immune system not to attack it. This is quite a difficult thing to achieve, as our immune cells have evolved to detect and destroy any type of bacteria they find. But teaching our immune systems to self-regulate and to refrain from attacking things that are harmless or actually good for us is a valuable lesson that can help prevent both allergies and autoimmune diseases.

The concept of microbiota helping to educate and develop our immune systems is known as the Old Friends hypothesis. This idea explains the dependence of our immune system development on the close presence of different types of bacteria, not necessarily harmful for us, and so it has now replaced the hygiene hypothesis.

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So if these microbes live with us, how come our immune systems are not getting proper training? Microbiota diversity – the different kinds of bacteria and other microbes that live inside us – has been steadily declining since the 1960s. This is due to a number of different factors, including life in an urban as opposed to rural environment, less exposure to the outdoors, a less diverse diet incorporating highly processed foods and extensive use of antibiotics.

Factors that affect life in the first few months are also critical because exposure to microbiota needs to start as early as possible - when our immune systems are developing and maturing, in fact. These include an increased proportion of births by C-section (which means that babies do not interact with the vaginal microbiota as they are born ) and decreased rates of breastfeeding, which provides maternal microbes through milk.

Our love for detergents that kill 99 percent of bacteria is not solely to blame for making us sick and it is important to teach our children basic hygiene. Washing hands after going to the toilet or before eating can indeed prevent serious infections. But changes in lifestyle that encourage our microbiota to be as diverse as possible from a very early age will reinforce the function of our immune system, making it the best army it can be.

The views expressed here are those of the author and do not represent or reflect the views of RTÉ